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Chlorine in PDB 5gwi: Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

Enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

All present enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R:
5.99.1.3;

Protein crystallography data

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi was solved by Y.R.Wang, S.F.Chen, C.C.Wu, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.788, 176.966, 94.528, 90.00, 112.30, 90.00
R / Rfree (%) 21.4 / 25.3

Other elements in 5gwi:

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Platinum (Pt) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R (pdb code 5gwi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5gwi

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Chlorine binding site 1 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1301

b:55.6
occ:0.50
 CL1 A:N2R1301 0.0 55.6 0.5
CL1 A:N2N1302 0.4 50.3 0.5
PT A:N2R1301 2.3 83.6 0.5
PT1 A:N2N1302 2.3 85.3 0.5
N13 A:N2N1302 2.7 83.1 0.5
N13 A:N2R1301 2.9 82.8 0.5
CG A:GLN778 3.4 46.7 1.0
CL2 A:N2R1301 3.5 0.8 0.5
CE A:MET781 3.8 50.4 1.0
CL2 A:N2N1302 3.8 0.3 0.5
O A:GLN778 3.9 37.6 1.0
CG A:PRO819 4.0 41.9 1.0
C02 A:N2N1302 4.1 75.8 0.5
CA A:GLN778 4.1 33.6 1.0
CB A:GLN778 4.3 40.3 1.0
N09 A:N2N1302 4.3 84.3 0.5
N09 A:N2R1301 4.3 82.6 0.5
CD A:GLN778 4.3 67.3 1.0
C02 A:N2R1301 4.4 73.0 0.5
NE2 A:GLN778 4.4 64.8 1.0
C A:GLN778 4.4 45.4 1.0
CB A:MET781 4.5 43.3 1.0
CD A:PRO819 4.6 40.4 1.0
O4 D:DT9 4.6 69.9 1.0
CG A:MET782 4.7 68.0 1.0
C10 A:N2N1302 4.8 77.5 0.5
C10 A:N2R1301 4.9 77.5 0.5
SD A:MET781 4.9 58.0 1.0

Chlorine binding site 2 out of 8 in 5gwi

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Chlorine binding site 2 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1301

b:0.8
occ:0.50
 CL2 A:N2R1301 0.0 0.8 0.5
CL2 A:N2N1302 0.4 0.3 0.5
PT1 A:N2N1302 2.2 85.3 0.5
PT A:N2R1301 2.3 83.6 0.5
N09 A:N2R1301 2.9 82.6 0.5
N09 A:N2N1302 3.1 84.3 0.5
CL1 A:N2N1302 3.2 50.3 0.5
SD A:MET782 3.4 0.0 1.0
CL1 A:N2R1301 3.5 55.6 0.5
CG A:MET782 3.5 68.0 1.0
CA A:MET782 4.0 31.2 1.0
CE A:MET782 4.1 71.0 1.0
N13 A:N2N1302 4.2 83.1 0.5
N13 A:N2R1301 4.3 82.8 0.5
C10 A:N2R1301 4.3 77.5 0.5
C10 A:N2N1302 4.3 77.5 0.5
CB A:MET782 4.3 48.6 1.0
N A:MET782 4.4 50.5 1.0
CG A:PRO819 4.5 41.9 1.0
O A:MET781 4.6 37.4 1.0
C A:MET781 4.7 45.5 1.0
C02 A:N2N1302 4.9 75.8 0.5
CG2 A:VAL785 4.9 24.1 1.0
C02 A:N2R1301 4.9 73.0 0.5

Chlorine binding site 3 out of 8 in 5gwi

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Chlorine binding site 3 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1302

b:50.3
occ:0.50
 CL1 A:N2N1302 0.0 50.3 0.5
CL1 A:N2R1301 0.4 55.6 0.5
PT A:N2R1301 2.3 83.6 0.5
PT1 A:N2N1302 2.3 85.3 0.5
N13 A:N2N1302 2.9 83.1 0.5
N13 A:N2R1301 3.2 82.8 0.5
CL2 A:N2R1301 3.2 0.8 0.5
CL2 A:N2N1302 3.5 0.3 0.5
CG A:GLN778 3.6 46.7 1.0
O A:GLN778 3.6 37.6 1.0
CE A:MET781 3.8 50.4 1.0
CG A:PRO819 3.9 41.9 1.0
CA A:GLN778 4.1 33.6 1.0
CB A:MET781 4.1 43.3 1.0
N09 A:N2R1301 4.3 82.6 0.5
C A:GLN778 4.3 45.4 1.0
N09 A:N2N1302 4.3 84.3 0.5
C02 A:N2N1302 4.3 75.8 0.5
CB A:GLN778 4.3 40.3 1.0
CD A:GLN778 4.4 67.3 1.0
CG A:MET782 4.4 68.0 1.0
NE2 A:GLN778 4.5 64.8 1.0
CD A:PRO819 4.6 40.4 1.0
N A:MET782 4.6 50.5 1.0
C02 A:N2R1301 4.6 73.0 0.5
SD A:MET781 4.9 58.0 1.0
C10 A:N2N1302 4.9 77.5 0.5
C A:MET781 4.9 45.5 1.0

Chlorine binding site 4 out of 8 in 5gwi

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Chlorine binding site 4 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1302

b:0.3
occ:0.50
 CL2 A:N2N1302 0.0 0.3 0.5
CL2 A:N2R1301 0.4 0.8 0.5
PT1 A:N2N1302 2.3 85.3 0.5
PT A:N2R1301 2.4 83.6 0.5
N09 A:N2R1301 2.7 82.6 0.5
N09 A:N2N1302 2.9 84.3 0.5
SD A:MET782 3.5 0.0 1.0
CL1 A:N2N1302 3.5 50.3 0.5
CG A:MET782 3.8 68.0 1.0
CL1 A:N2R1301 3.8 55.6 0.5
CE A:MET782 4.1 71.0 1.0
C10 A:N2R1301 4.2 77.5 0.5
C10 A:N2N1302 4.2 77.5 0.5
N13 A:N2N1302 4.3 83.1 0.5
CA A:MET782 4.3 31.2 1.0
N13 A:N2R1301 4.4 82.8 0.5
CG A:PRO819 4.6 41.9 1.0
CB A:MET782 4.6 48.6 1.0
N A:MET782 4.7 50.5 1.0
C02 A:N2N1302 4.9 75.8 0.5
C02 A:N2R1301 4.9 73.0 0.5
O A:MET781 4.9 37.4 1.0
CG2 A:VAL785 4.9 24.1 1.0

Chlorine binding site 5 out of 8 in 5gwi

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Chlorine binding site 5 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1301

b:55.1
occ:0.50
 CL1 B:N2R1301 0.0 55.1 0.5
CL1 B:N2N1302 0.4 53.0 0.5
PT B:N2R1301 2.3 66.9 0.5
PT1 B:N2N1302 2.3 96.0 0.5
N13 B:N2N1302 2.8 79.8 0.5
N13 B:N2R1301 2.9 77.8 0.5
CG B:GLN778 3.4 52.5 1.0
CL2 B:N2R1301 3.5 0.3 0.5
O B:GLN778 3.6 37.6 1.0
CL2 B:N2N1302 3.7 0.1 0.5
CE B:MET781 3.7 62.0 1.0
CA B:GLN778 3.9 40.9 1.0
C02 B:N2N1302 4.1 69.6 0.5
CB B:GLN778 4.1 46.0 1.0
CG B:PRO819 4.2 46.9 1.0
CB B:MET781 4.2 32.0 1.0
C B:GLN778 4.2 46.2 1.0
N09 B:N2N1302 4.3 75.3 0.5
N09 B:N2R1301 4.3 74.0 0.5
C02 B:N2R1301 4.3 66.4 0.5
CD B:GLN778 4.4 59.8 1.0
CG B:MET782 4.4 48.5 1.0
NE2 B:GLN778 4.6 51.4 1.0
O4 F:DT9 4.6 61.1 1.0
N B:MET782 4.7 53.3 1.0
CD B:PRO819 4.7 41.4 1.0
C10 B:N2N1302 4.7 70.2 0.5
SD B:MET781 4.9 60.2 1.0
C10 B:N2R1301 4.9 70.5 0.5
C B:MET781 5.0 43.6 1.0

Chlorine binding site 6 out of 8 in 5gwi

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Chlorine binding site 6 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1301

b:0.3
occ:0.50
 CL2 B:N2R1301 0.0 0.3 0.5
CL2 B:N2N1302 0.2 0.1 0.5
PT1 B:N2N1302 2.2 96.0 0.5
PT B:N2R1301 2.3 66.9 0.5
N09 B:N2R1301 2.9 74.0 0.5
N09 B:N2N1302 2.9 75.3 0.5
CL1 B:N2N1302 3.4 53.0 0.5
SD B:MET782 3.4 0.1 1.0
CL1 B:N2R1301 3.5 55.1 0.5
CG B:MET782 3.6 48.5 1.0
CE B:MET782 4.0 67.9 1.0
C10 B:N2N1302 4.2 70.2 0.5
N13 B:N2N1302 4.2 79.8 0.5
CA B:MET782 4.2 33.3 1.0
N13 B:N2R1301 4.3 77.8 0.5
C10 B:N2R1301 4.3 70.5 0.5
CB B:MET782 4.5 49.2 1.0
N B:MET782 4.6 53.3 1.0
O B:MET781 4.8 36.0 1.0
C02 B:N2N1302 4.8 69.6 0.5
CG2 B:VAL785 4.8 30.2 1.0
C B:MET781 4.9 43.6 1.0
C02 B:N2R1301 4.9 66.4 0.5
CD B:PRO819 5.0 41.4 1.0

Chlorine binding site 7 out of 8 in 5gwi

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Chlorine binding site 7 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1302

b:53.0
occ:0.50
 CL1 B:N2N1302 0.0 53.0 0.5
CL1 B:N2R1301 0.4 55.1 0.5
PT1 B:N2N1302 2.3 96.0 0.5
PT B:N2R1301 2.4 66.9 0.5
N13 B:N2N1302 2.9 79.8 0.5
N13 B:N2R1301 3.1 77.8 0.5
CL2 B:N2R1301 3.4 0.3 0.5
CL2 B:N2N1302 3.5 0.1 0.5
CE B:MET781 3.6 62.0 1.0
CG B:PRO819 3.8 46.9 1.0
CG B:GLN778 3.9 52.5 1.0
O B:GLN778 3.9 37.6 1.0
CB B:MET781 4.0 32.0 1.0
CA B:GLN778 4.2 40.9 1.0
CD B:PRO819 4.3 41.4 1.0
N09 B:N2N1302 4.3 75.3 0.5
C02 B:N2N1302 4.3 69.6 0.5
N09 B:N2R1301 4.3 74.0 0.5
C02 B:N2R1301 4.5 66.4 0.5
C B:GLN778 4.5 46.2 1.0
CB B:GLN778 4.5 46.0 1.0
CG B:MET782 4.6 48.5 1.0
SD B:MET781 4.7 60.2 1.0
N B:MET782 4.7 53.3 1.0
O4 F:DT9 4.7 61.1 1.0
CB B:PRO819 4.8 35.7 1.0
CD B:GLN778 4.8 59.8 1.0
C B:MET781 4.9 43.6 1.0
C10 B:N2N1302 4.9 70.2 0.5
CG B:MET781 4.9 45.6 1.0
NE2 B:GLN778 5.0 51.4 1.0

Chlorine binding site 8 out of 8 in 5gwi

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Chlorine binding site 8 out of 8 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1302

b:0.1
occ:0.50
 CL2 B:N2N1302 0.0 0.1 0.5
CL2 B:N2R1301 0.2 0.3 0.5
PT1 B:N2N1302 2.3 96.0 0.5
PT B:N2R1301 2.4 66.9 0.5
N09 B:N2N1302 2.9 75.3 0.5
N09 B:N2R1301 2.9 74.0 0.5
CL1 B:N2N1302 3.5 53.0 0.5
SD B:MET782 3.6 0.1 1.0
CL1 B:N2R1301 3.7 55.1 0.5
CG B:MET782 3.8 48.5 1.0
CE B:MET782 4.2 67.9 1.0
C10 B:N2N1302 4.2 70.2 0.5
N13 B:N2N1302 4.3 79.8 0.5
CA B:MET782 4.3 33.3 1.0
C10 B:N2R1301 4.4 70.5 0.5
N13 B:N2R1301 4.4 77.8 0.5
CB B:MET782 4.7 49.2 1.0
N B:MET782 4.7 53.3 1.0
CG2 B:VAL785 4.7 30.2 1.0
O B:MET781 4.8 36.0 1.0
C02 B:N2N1302 4.9 69.6 0.5
CD B:PRO819 4.9 41.4 1.0
C B:MET781 5.0 43.6 1.0
C02 B:N2R1301 5.0 66.4 0.5

Reference:

Y.R.Wang, S.F.Chen, C.C.Wu, Y.W.Liao, T.S.Lin, K.T.Liu, Y.S.Chen, T.K.Li, T.C.Chien, N.L.Chan. Producing Irreversible Topoisomerase II-Mediated Dna Breaks By Site-Specific Pt(II)-Methionine Coordination Chemistry Nucleic Acids Res. V. 45 10861 2017.
ISSN: ESSN 1362-4962
PubMed: 28977631
DOI: 10.1093/NAR/GKX742
Page generated: Fri Jul 26 08:37:09 2024

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